From 5a9dbe5d7c5472f3001f5c860ce498b97b073ce4 Mon Sep 17 00:00:00 2001
From: phue <patrick.huether@gmail.com>
Date: Mon, 28 Oct 2019 14:11:34 +0100
Subject: [PATCH] MENDEL is no more

the cluster is no longer operational, was replaced by CBE
---
 README.md            |  1 -
 conf/mendel.config   | 24 ------------------------
 docs/mendel.md       | 18 ------------------
 nfcore_custom.config |  1 -
 4 files changed, 44 deletions(-)
 delete mode 100644 conf/mendel.config
 delete mode 100644 docs/mendel.md

diff --git a/README.md b/README.md
index 451c12f..20fafd7 100644
--- a/README.md
+++ b/README.md
@@ -95,7 +95,6 @@ Currently documentation is available for the following clusters:
 * [GIS](docs/gis.md)
 * [HEBBE](docs/hebbe.md)
 * [KRAKEN](docs/kraken.md)
-* [MENDEL](docs/mendel.md)
 * [MUNIN](docs/munin.md)
 * [PASTEUR](docs/pasteur.md)
 * [PHOENIX](docs/phoenix.md)
diff --git a/conf/mendel.config b/conf/mendel.config
deleted file mode 100644
index 0fb7e81..0000000
--- a/conf/mendel.config
+++ /dev/null
@@ -1,24 +0,0 @@
-//Profile config names for nf-core/configs
-params {
-  config_profile_description = 'GMI MENDEL cluster profile provided by nf-core/configs'
-  config_profile_contact = 'Patrick Hüther (@phue)'
-  config_profile_url = 'http://www.gmi.oeaw.ac.at/'
-}
-
-manifest {
-  nextflowVersion = '>=19.01.0'
-}
-
-process {
-  beforeScript = 'module load Miniconda3/4.6.7'
-  executor = 'pbspro'
-  clusterOptions = { "-P $params.project" }
-}
-
-params {
-  max_cpus = 32
-  max_memory = 128.GB
-  max_time = 192.h
-  igenomes_ignore = true
-  igenomesIgnore = true //deprecated
-}
diff --git a/docs/mendel.md b/docs/mendel.md
deleted file mode 100644
index ae0ad4c..0000000
--- a/docs/mendel.md
+++ /dev/null
@@ -1,18 +0,0 @@
-# nf-core/configs: MENDEL Configuration
-
-All nf-core pipelines have been successfully configured for use on the MENDEL CLUSTER at the Gregor Mendel Institute (GMI).
-
-To use, run the pipeline with `-profile conda,mendel`. This will download and launch the [`mendel.config`](../conf/mendel.config) which has been pre-configured with a setup suitable for the MENDEL cluster. A Conda environment will be created automatically and software dependencies will be resolved via [bioconda](https://bioconda.github.io/).
-
-Before running the pipeline you will need to load Conda using the environment module system on MENDEL. You can do this by issuing the commands below:
-
-```bash
-## Load Nextflow and Conda environment modules
-module purge
-module load Nextflow
-module load Miniconda/4.6.7
-```
-
->NB: You will need an account to use the HPC cluster in order to run the pipeline. If in doubt contact the HPC team.
-
->NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact the HPC team.
diff --git a/nfcore_custom.config b/nfcore_custom.config
index 06182f5..12a0c1e 100644
--- a/nfcore_custom.config
+++ b/nfcore_custom.config
@@ -25,7 +25,6 @@ profiles {
   gis          { includeConfig "${params.custom_config_base}/conf/gis.config" }
   hebbe        { includeConfig "${params.custom_config_base}/conf/hebbe.config" }
   kraken       { includeConfig "${params.custom_config_base}/conf/kraken.config" }
-  mendel       { includeConfig "${params.custom_config_base}/conf/mendel.config" }
   munin        { includeConfig "${params.custom_config_base}/conf/munin.config" }
   pasteur      { includeConfig "${params.custom_config_base}/conf/pasteur.config" }
   phoenix      { includeConfig "${params.custom_config_base}/conf/phoenix.config" }